A major question in evolutionary biology, determining the genetic source of biodiversity, is best answered by examining species at the interface of speciation - closely related species that are known to hybridize. Recent genetic advances have highlighted the pervasiveness of hybridization in these species. Further, dense marker analysis shows that genetic exchange between species is not uniformly distributed across the genome. This proposal aims to understand which factors contribute to this regional variation in gene flow across the genetic landscape. Much work in speciation has been focused on understanding those factors that produce barriers to reproduction, focusing particularly on regions where divergence between species is high. These regions may correspond to speciation genes that are selected against in different genetic backgrounds, or structural variants such as chromosomal inversions that limit interspecies gene exchange. Beyond inversions, no structural features have been identified which commonly differentiate recently diverged species. Our research proposes to survey many hybridizing taxa and understand what contributes to variation in genetic exchange between species. Specifically, we propose to computationally predict recombination rate differences in hybrids relative to within species linkage maps. We will then determine if changes in hybrid recombination rates (as compared to within-species recombination rates) are associated with changes in between species nucleotide divergence. We predict that this correlation will highlight regions of the genome important in speciation. These changes could be due to genetic variants that act like inversions to prevent hybrid alleles from being incorporated into the genome. Therefore, we plan to dissect these regions in our survey of taxa and examine if these feature any common genetic elements that distinguish recently diverged species could contribute to the pattern. Recent research in humans has revealed extensive evidence of genomic structural variation within and between individuals. Some of these variants have been connected to disease; however, our overall understanding of the role of these variants in contributing to the structure of our genome is still limited. Our stuy aims to understand if these variants play a role in facilitating speciation by disrupting genetic exchange, which has also been linked to disease. By making use of existing data in a variety of biological systems, the results of our research have the potential to make predictions about which regions of the genome are likely to be important in speciation in other research systems.